The whole thing had been a horrible mistake by the U.S. Department of Defense. Kevin Drum takes it from there:
[H]e wasn't released for several more years, and then only after the newly elected German chancellor made a personal appeal to George Bush. But why? Why didn't they release him earlier?Remember, George W. Bush and his administration is doing this in our name, we the people of the United States:
One can never rule out bureaucratic ineptitude, but the more likely explanation is that they were afraid he'd tell the world about his treatment. So they just kept him locked up instead.